Answers to your questions:

1. To specify which modules are loaded automatically at boot time, edit the file 
/etc/modules. Each line of /etc/modules is one module; note that module names are 
listed without their .o suffixes.

2. System.map is a hexadecimal index to functions in the kernel. It's a plain text 
file, so you can open it up with an editor and take a look. It isn't required for 
normal operation, but might be useful for debugging.

3. If you compiled the kernel, you already have kernel headers (so you don't need the 
separate package). They are found in kernel-source-x.y.z/include.

4. Yes, new modules will overwrite old ones. To avoid this, edit the top-level 
Makefile and add something meaningful to "EXTRAVERSION=" before you compile your 
kernel or modules. I use some version of the date, like "EXTRAVERSION=.0308". I copy 
the kernel image to /boot/bzImage-2.4.20.0308, and the System.map to 
/boot/System.map-2.4.20.0308. When I do "make modules_install" the modules will be 
copied to /lib/modules/2.4.20.0308, and my other 2.4.20 modules will be left intact.

A nice side effect of this method of specifying EXTRAVERSION is that after I do 
"update-grub", the kernels will be arranged in the grub boot menu with the latest 
first.

But of course I don't really do it as above. I use make-kpkg.

Kevin


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